1. What species does BioGPS support?

Currently, BioGPS supports seven species: human (H. sapiens), mouse (M. musculus), rat (R. norvegicus), fruitfly (D. melanogaster), roundworm (C. elegans), zebrafish (D. rerio) and thale cress (A. thaliana). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database.

For plugins that contain data for multiple species, users can switch between allowed species using the species selector in the upper-right corner of the plugin window, as shown at right. Species which are grayed-out mean either that the species does not have an ortholog for that gene, or that the selected plugin does not provide data for that species.

2. How do I cite BioGPS in my paper?

The manuscript describing BioGPS has been published in Genome Biology. Note that when referencing any of the expression data sets in BioGPS, you should also include a citation to the relevant paper describing those data. Please see the Publications section on our Downloads page.

3. How do I deep link to BioGPS?

Deep links (or permalinks) are most easily generated based on Entrez Gene ID. For example, for the gene CDK2 (Entrez Gene ID = 1017):

• http://biogps.gnf.org/gene/1017/

Queries based on identifiers can also be constructed using URLs like this:

• http://biogps.gnf.org/?query=CDK2 (searches by symbols, identifiers, and aliases only)
• http://biogps.gnf.org/?query=CDK2&qtype=keyword (searches all text fields)

If additional linking mechanisms are required, please contact us.

4. What features are available for users who have created an account?

5. What kind of gene identifiers are supported for a query?

In addition to official symbols and aliases, BioGPS supports most common public gene identifiers, including Entrez Gene, Ensembl, Uniprot, Refseq, UniGene, Gene Ontology, PDB, and Interpro. In addition, users can search by Affymetrix probe set identifiers from many common gene expression chip types (U133, MOE430, U95, RGU34, GNF1H and GNF1M).

6. Help! There are too many scrollbars!

Although not technically a question, this is a frequently heard frustration. Undoubtedly BioGPS works better on higher-resolution monitors, but we also have some pretty effective strategies for limiting scrollbar overload for all users.

1. First, use fewer plugins per layout. In fact, we often create layouts with just a single plugin.
2. Second, use the maximize plugin button in the upper right of the plugin window, which will show one plugin in a large size while freezing the main browser scrollbar.
3. Third, use the "Open in browser" option under the "more options" plugin menu. This option will open the plugin in a new browser tab or window.
4. Fourth, use the "Open all in browser" feature under the layout options menu. Selecting this option will load all plugins, each in its own browser tab or window.

7. What are the units of expression?

Expression values from Affymetrix chips relate to fluorescence intensity. Since there are multiple probes for each transcript on the microarray, these intensity values are summarized using various data processing algorithms. In our case, we mostly use gcrma.

8. Can I compare values across tissues? across probe sets?

Since each probe and probe set has different background characteristics (depending of cross hybridization, secondary structure, etc.), comparing expression values across different probesets in a single sample is generally not recommended. Microarrays are primarily suited for comparing single probesets across multiple samples.